To check available detectors:

available_detectors
#> [1] "Excalibur"              "PerkinElmerFull"       
#> [3] "PerkinElmerCropped1600" "PerkinElmerRefurbished"
#> [5] "Pilatus"

To create detector object

pilatus_detector <- create_module("Pilatus")

To visualise detector object

plot_detector(pilatus_detector)

Detector analysis

plot_pixel_ctr_eucl(pilatus_detector)

plot_pixel_ctr_linf(pilatus_detector)

plot_pixel_dist_corner(pilatus_detector)

plot_pixel_dist_edge_col(pilatus_detector)

plot_pixel_dist_edge_row(pilatus_detector)

plot_pixel_dist_edge(pilatus_detector)

Importing user-defined detector

user_def_detector <- readin_detector("../inst/extdata/user-defined.dc")

plot_detector(user_def_detector)

To upload pixel file

pilatus_detector <- create_module("Pilatus")

file_path <- "../inst/extdata/Pilatus/badpixel_mask.tif"

pilatus_detector <- load_pix_matrix(detector = pilatus_detector, file_path = file_path)

plot_detector_damaged(detector = pilatus_detector, caption = FALSE)

plot_detector_module_damaged(detector = pilatus_detector, col = 4, row = 5, caption = FALSE)

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_damaged(detector = detector_perkin)

detector_exc <- create_module("Excalibur")

file_path <- c("../inst/extdata/Excalibur/pixelmask.fem1.hdf", 
               "../inst/extdata/Excalibur/pixelmask.fem2.hdf",
               "../inst/extdata/Excalibur/pixelmask.fem3.hdf",
               "../inst/extdata/Excalibur/pixelmask.fem4.hdf",
               "../inst/extdata/Excalibur/pixelmask.fem5.hdf",
               "../inst/extdata/Excalibur/pixelmask.fem6.hdf")

detector_exc <- load_pix_matrix(detector = detector_exc, file_path = file_path)

plot_detector_damaged(detector = detector_exc)

Damaged pixel density

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_density(detector = detector_perkin, adjust = 0.5)

plot_detector_density(detector = detector_perkin, adjust = 0.5, row = 1, col = 2)

Summaries

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

cat(detector_summary(detector_perkin))
#> Detector: 
#>   Name:  PerkinElmerFull 
#>   Date:  NA 
#>   Width:  2000 
#>   Height:  2000 
#>   Number of columns in array of module (= number of modules per row):  16 
#>   Number of rows in array of module (= number of modules per column):  2 
#>   Widths of modules:  104 128 128 128 128 128 128 128 128 128 128 128 128 128 128 104 
#>   Heights of modules:  1000 1000 
#>   Widths of gaps between modules:  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
#>   Heights of gaps between modules:  0 
#> 
cat(dead_stats_summary(detector_perkin))
#> Total number of damaged pixels:  9451 
#>   Total number of modules:  32 
#>   Average number of damaged pixels per module:  295.3 
#>   
#>   Chi-Squared Test results:
#>   Xsq =  23280.5170881388 , Xsq df =  31 , Xsq p =  0 
#> 

Damaged pixel counts per module

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

detector_perkin <- get_dead_stats(detector_perkin)

plot_detector_cnt_mod(detector = detector_perkin, caption = FALSE)

plot_detector_cnt_mod(detector = detector_perkin, row = 1, col = 5, caption = FALSE)

Arrows

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_arrows(detector = detector_perkin)

plot_detector_arrows(detector = detector_perkin, row = 1, col = 5)

K, F, G plots

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_kfg(detector = detector_perkin, func = "K", caption = FALSE)
#> number of data points exceeds 3000 - computing border correction estimate only

plot_detector_kfg(detector = detector_perkin, func = "F")

plot_detector_kfg(detector = detector_perkin, func = "G")

plot_detector_kfg(detector = detector_perkin, func = "K", row = 1, col = 5, caption = FALSE)

plot_detector_kfg(detector = detector_perkin, func = "F", row = 1, col = 5, caption = FALSE)

plot_detector_kfg(detector = detector_perkin, func = "G", row = 1, col = 5, caption = FALSE)

Inhomogenious K, F, G plots

detector_pilatus <- create_module("Pilatus")

file_path <- "../inst/extdata/Pilatus/badpixel_mask.tif"

detector_pilatus <- load_pix_matrix(detector = detector_pilatus, file_path = file_path)

plot_detector_kfg(detector = detector_pilatus, func = "Kinhom")

plot_detector_kfg(detector = detector_pilatus, func = "Finhom")

plot_detector_kfg(detector = detector_pilatus, func = "Ginhom")

plot_detector_kfg(detector = detector_pilatus, func = "Kinhom", row = 1, col = 5, caption = FALSE)

plot_detector_kfg(detector = detector_pilatus, func = "Finhom", row = 1, col = 5, caption = FALSE)

plot_detector_kfg(detector = detector_pilatus, func = "Ginhom", row = 1, col = 5, caption = FALSE)

Events

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_damaged(detector = detector_perkin)

incl_event_list <- list(1,2,3,4,5,6,7,8)
      
detector_events <- detectorchecker::find_clumps(detector_perkin)
#> Loading required namespace: igraph
      
detectorchecker::plot_events(detector_events, caption = FALSE, incl_event_list = incl_event_list)

row_ = 2
col_ = 3

detector_events <- detectorchecker::find_clumps(detector_perkin, row = row_, col = col_)

plot_module_events(detector_events, row = row_, col = col_, caption = FALSE, 
                   incl_event_list = incl_event_list)

### Events analysis

detector_events <- detectorchecker::find_clumps(detector_perkin)
detectorchecker::plot_events_arrows(detector_events, caption = FALSE, incl_event_list = incl_event_list)

Events with selected rows and cols

detector_events <- detectorchecker::find_clumps(detector_perkin, row = row_, col = col_)

detectorchecker::plot_events_density(detector_events, row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

detectorchecker::plot_events_arrows(detector_events, row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

detectorchecker::plot_events_angles(detector_events, row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

detectorchecker::plot_events_kfg(detector_events, func = "K", row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

detectorchecker::plot_events_kfg(detector_events, func = "Kinhom", row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

detectorchecker::plot_events_count(detector_events, row = row_, col = col_, caption = FALSE, incl_event_list = incl_event_list)

Removing areas of high density pixel damage from the analysis

detector_perkin <- create_module("PerkinElmerFull")

file_path <- "../inst/extdata/PerkinElmer_Full/BadPixelMap.bpm/BadPixelMap_t1.bpm.xml"

detector_perkin <- load_pix_matrix(detector = detector_perkin, file_path = file_path)

plot_detector_damaged(detector = detector_perkin)

detector_perkin_modified <- remove_high_density_cluster(detector_perkin, min_pts = 30, eps_adjust = 0.05)

plot_detector_damaged(detector = detector_perkin_modified)